Early Professional Development
Name: Phil Xie
Institute: Department of Molecular Biophysics and Biochemistry
University: Yale University
Period: Summer, 2014
Early Professional Development
This summer, I am fortunate to work in Gerstein Lab, the largest bioinformatics lab in Yale. Bioinformatics is getting increasingly important in medical field, one reason of which is that it helps doctors study large data, such as those from sequencing and microarray. It is a promising tool that can be used to visualize personal medicine in near future.
My project is related to identifying enhancer, which is a part of the ENCODE Consortium. Enhancers are essential DNA sequences which are involved in controlling transcription, and ultimately the cell's function and identity. However, unlike coding sequences, it is humanly impossible to tell whether a piece of unknown DNA is enhancer or not, without actually testing it in labs. This is particularly the question we need to answer when analyzing cancer genomics, because we want to know whether the mutation found is causing cancer. Thus, developing a tool to quickly identify enhancers is very meaningful.
Members of the Consortium have already developed prototypes using machine learning, which is a type of artificial intelligence, and have made predictions for enhancers across the whole genome. My work is to analyze the performance of these prototypes, and thus help in further development of the tools. In the process, I wrote programming scripts in Python and R (two commonly used programming language), and ran them on Yale's supercomputer.
With effort in my project, reading papers, and communication with other lab members, I learnt how bioinformatics can help both doctors and researchers. Also, since most works are done on computer, international collaboration is possible.
Last but not least, I must thank the Faculty for giving me this opportunity, and Professor Mark Gerstein for accepting me into his lab. I am most grateful to be in a lab with wonderful lab culture and members from diverse backgrounds.
